I don't have any docs set up and ready to use, but here are some instructions that should get you started. doug
------------------------------------------------------------------------------------------------------- Download these files ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.tar.gz # Copy surfreg and xhemireg into $FREESURFER_HOME/bin # Untar fsaverage_sym.tar.gz into your $SUBJECTS_DIR cd $SUBJECTS_DIR tar xvfz fsaverage_sym.tar.gz --------------------------------------------------------- To apply an existing atlas (eg, fsaverage_sym) to an anatomical analysis # Reg to atlas (1-2 hours per subject) # Creates $subject/xhemi # Creates lh.fsaverage_sym.sphere.reg in $subject and $subject/xhemi foreach subject (subjectlist) surfreg --s $subject --t fsaverage_sym --lh surfreg --s $subject --t fsaverage_sym --lh --xhemi end # Create a stack of subjects mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.sm00.mgh \ --s subj1 --s subj2 ... # Smooth mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm 5\ --i lh.lh-rh.thickness.sm00.mgh --o lh.lh-rh.thickness.sm05.mgh # Test mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir glm.lh.lh-rh.thickness.sm05 \ --osgm --surf fsaverage_sym lh # View tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh # Correct for MC (need new version of mri_glmfit-sim) mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 \ --cwpvalthresh .5 --cache 2 abs \ --subject-override fsaverage --------------------------------------------------------- # To apply an existing atlas to an arbitray volume data set: bbregister --s subject --reg register.dat ... mri_vol2surf --reg register.dat --mov data.nii.gz --hemi lh --o data.lh.nii mri_vol2surf --reg register.dat --mov data.nii.gz --hemi rh --o data.rh.nii # Map lh data to fsaverage_sym mri_surf2surf --srcsubject subject --srcsurfreg fsaverage_sym.sphere.reg \ --trgsubject fsaverage_sym --trgsurfreg sphere.reg --hemi lh --sval data.lh.nii \ --tval data.lh.fsaverage_sym.nii # Map rh data to fsaverage_sym. Note: (1) "subject" is subject/xhemi # and (2) The hemi (--hemi lh) is still lh not rh. mri_surf2surf --srcsubject subject/xhemi --srcsurfreg fsaverage_sym.sphere.reg \ --trgsubject fsaverage_sym --trgsurfreg sphere.reg --hemi lh --sval data.rh.nii \ --tval data.rh.fsaverage_sym.nii data.lh.fsaverage_sym.nii and data.rh.fsaverage_sym.nii are now in voxel-for-voxel registration. Andy Mayer wrote: > > Hello- > > > > Trying this post again. I would like to directly compare > asymmetries in FMRI activation in surface space based on the Greve et > al poster presented at HBM this year. We would like to register each > subject’s T1 data to the contralateral hemisphere of fsaverage and > made templates of the contra (?h.con.sphere.reg ) and ipsilateral > (?h.sphere.reg ) registrations. Is the following correct for the cross > hemisphere registration? Thanks > > > > mris_register -reverse -curv surf/rh.sphere > {$FREESURFER_HOME}/average/lh.average.curvature.filled.buckner40.tif > surf/rh.CON.sphere.reg > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
